{ "schema": "dia-health-one.nnc2215-physiological-charge-states.v1", "run": { "audit_script": "research/audit_nnc2215_physiological_charge_states.py", "input_graph": "research/data/nnc2215-full-conjugate-graph.json", "input_graph_sha256": "fb9feaed3537196515c62656d890c0e92b42c9b7da15955dd516b1d82dd178dc", "pH_reference": 7.4, "method": "Group-level formal-charge and proton-count bookkeeping from the neutral graph; no coordinates or pKa model used." }, "representation_boundaries": { "scope": "Conditional pH 7.4 candidate charge-state ledger for the source-derived full desB30 insulin\u2013NNC2215 neutral constitutional graph.", "not_a_prediction": "No pKa values, Boltzmann populations, or experimentally measured microstate are assigned.", "not_force_field_ready": "Formal charges are summed at functional-group level. No atom-localized partial charges, atom types, Lennard-Jones parameters, counterions, or solvent are provided.", "coordinate_usage": "No coordinate files were read or edited; coordinates do not select any atom map or site state.", "oxygen_labeling": "Carboxylate charge belongs to the functional group; no carbonyl versus anionic oxygen label is selected." }, "neutral_input": { "schema": "dia-health-one.nnc2215-full-conjugate-graph.v1", "formula": "C325H461N79O97S6", "total_formal_charge": 0, "hydrogen_count": 461 }, "fixed_conventional_assumptions": { "description": "These conventional ionization assignments are fixed for this bookkeeping envelope; local protein and macrocycle pKa shifts are not modeled.", "groups": [ { "site_id": "glu_A4", "label": "Glu A4 sidechain carboxyl", "site_type": "fixed_carboxylate_assumption", "atom_node_ids": [ "atom_0026", "atom_0027", "atom_0028" ], "atom_names": [ "CD", "OE1", "OE2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 } ] }, { "site_id": "glu_A17", "label": "Glu A17 sidechain carboxyl", "site_type": "fixed_carboxylate_assumption", "atom_node_ids": [ "atom_0126", "atom_0127", "atom_0128" ], "atom_names": [ "CD", "OE1", "OE2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 } ] }, { "site_id": "glu_B13", "label": "Glu B13 sidechain carboxyl", "site_type": "fixed_carboxylate_assumption", "atom_node_ids": [ "atom_0264", "atom_0265", "atom_0266" ], "atom_names": [ "CD", "OE1", "OE2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 } ] }, { "site_id": "glu_B21", "label": "Glu B21 sidechain carboxyl", "site_type": "fixed_carboxylate_assumption", "atom_node_ids": [ "atom_0323", "atom_0324", "atom_0325" ], "atom_names": [ "CD", "OE1", "OE2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 } ] }, { "site_id": "cterm_A21", "label": "Chain A C-terminal carboxyl", "site_type": "fixed_carboxylate_assumption", "atom_node_ids": [ "atom_0157", "atom_0158", "atom_0163" ], "atom_names": [ "C", "O", "OXT" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 } ] }, { "site_id": "cterm_B29", "label": "Chain B C-terminal carboxyl", "site_type": "fixed_carboxylate_assumption", "atom_node_ids": [ "atom_0391", "atom_0392", "atom_0398" ], "atom_names": [ "C", "O", "OXT" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 } ] }, { "site_id": "arg_B22", "label": "ArgB22 guanidinium", "site_type": "fixed_protonated_base_assumption", "atom_node_ids": [ "atom_0333", "atom_0334", "atom_0335", "atom_0336" ], "atom_names": [ "NE", "CZ", "NH1", "NH2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 4, "state_options": [ { "state": "protonated", "group_formal_charge": 1, "hydrogen_delta": 1 } ] } ], "group_formal_charge_delta": -5, "hydrogen_delta_from_neutral_graph": -5 }, "enumerated_variable_groups": [ { "site_id": "macrocycle_carboxyl_1", "label": "B29 macrocycle carboxyl 1", "site_type": "variable_carboxyl_group", "atom_node_ids": [ "atom_0499", "atom_0500", "atom_0501" ], "atom_names": null, "source_map_ids": [ 52, 53, 54 ], "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 }, { "state": "protonated", "group_formal_charge": 0, "hydrogen_delta": 0 } ] }, { "site_id": "macrocycle_carboxyl_2", "label": "B29 macrocycle carboxyl 2", "site_type": "variable_carboxyl_group", "atom_node_ids": [ "atom_0480", "atom_0481", "atom_0482" ], "atom_names": null, "source_map_ids": [ 60, 61, 62 ], "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 }, { "state": "protonated", "group_formal_charge": 0, "hydrogen_delta": 0 } ] }, { "site_id": "macrocycle_carboxyl_3", "label": "B29 macrocycle carboxyl 3", "site_type": "variable_carboxyl_group", "atom_node_ids": [ "atom_0438", "atom_0439", "atom_0440" ], "atom_names": null, "source_map_ids": [ 68, 69, 70 ], "neutral_graph_site_hydrogen_count": 1, "state_options": [ { "state": "deprotonated", "group_formal_charge": -1, "hydrogen_delta": -1 }, { "state": "protonated", "group_formal_charge": 0, "hydrogen_delta": 0 } ] }, { "site_id": "nterm_A1", "label": "A-chain GlyA1 N terminus", "site_type": "variable_ammonium_group", "atom_node_ids": [ "atom_0001" ], "atom_names": [ "N" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 2, "state_options": [ { "state": "protonated", "group_formal_charge": 1, "hydrogen_delta": 1 }, { "state": "neutral", "group_formal_charge": 0, "hydrogen_delta": 0 } ] }, { "site_id": "his_B5", "label": "HisB5 imidazole", "site_type": "variable_histidine_group", "atom_node_ids": [ "atom_0204", "atom_0205", "atom_0206", "atom_0207", "atom_0208" ], "atom_names": [ "CG", "ND1", "CD2", "CE1", "NE2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 3, "state_options": [ { "state": "neutral_template_tautomer", "tautomer": "epsilon2", "group_formal_charge": 0, "hydrogen_delta": 0 }, { "state": "neutral_alternate_tautomer", "tautomer": "delta1", "group_formal_charge": 0, "hydrogen_delta": 0 }, { "state": "protonated", "tautomer": "both_ring_nitrogens_protonated", "group_formal_charge": 1, "hydrogen_delta": 1 } ] }, { "site_id": "his_B10", "label": "HisB10 imidazole", "site_type": "variable_histidine_group", "atom_node_ids": [ "atom_0238", "atom_0239", "atom_0240", "atom_0241", "atom_0242" ], "atom_names": [ "CG", "ND1", "CD2", "CE1", "NE2" ], "source_map_ids": null, "neutral_graph_site_hydrogen_count": 3, "state_options": [ { "state": "neutral_template_tautomer", "tautomer": "epsilon2", "group_formal_charge": 0, "hydrogen_delta": 0 }, { "state": "neutral_alternate_tautomer", "tautomer": "delta1", "group_formal_charge": 0, "hydrogen_delta": 0 }, { "state": "protonated", "tautomer": "both_ring_nitrogens_protonated", "group_formal_charge": 1, "hydrogen_delta": 1 } ] } ], "excluded_sites": { "tyrosine_phenols": [ { "site_id": "tyr_A14_phenol", "label": "Tyr A14 phenol", "atom_node_id": "atom_0102", "assumed_state": "neutral", "reason": "Excluded from the conventional pH 7.4 baseline; no local pKa prediction or measurement is available." }, { "site_id": "tyr_A19_phenol", "label": "Tyr A19 phenol", "atom_node_id": "atom_0148", "assumed_state": "neutral", "reason": "Excluded from the conventional pH 7.4 baseline; no local pKa prediction or measurement is available." }, { "site_id": "tyr_B16_phenol", "label": "Tyr B16 phenol", "atom_node_id": "atom_0291", "assumed_state": "neutral", "reason": "Excluded from the conventional pH 7.4 baseline; no local pKa prediction or measurement is available." }, { "site_id": "tyr_B26_phenol", "label": "Tyr B26 phenol", "atom_node_id": "atom_0374", "assumed_state": "neutral", "reason": "Excluded from the conventional pH 7.4 baseline; no local pKa prediction or measurement is available." } ], "disulfide_cysteines": "All six cysteines are in the three declared disulfides; no free thiol state is included.", "modified_conjugate_endpoints": [ { "site_id": "conjugated_PheB1_N", "atom_node_id": "atom_0164", "graph_formal_charge": 0, "interpretation": "Acylated B-chain N terminus; not a free amine in this graph.", "hydrogen_ownership": "Unresolved in the candidate PDB records; this ledger does not change it." }, { "site_id": "conjugated_LysB29_NZ", "atom_node_id": "atom_0397", "graph_formal_charge": 0, "interpretation": "Carbamate-bound Lys epsilon nitrogen; not a free lysine amine in this graph." } ], "other_groups": "All remaining neutral amides, alcohols, ethers, triazole, and aromatic groups are held in their neutral graph states for this envelope." }, "canonical_candidate": { "state_id": "mcddd_a1p_h5t_h10t", "pH_reference": 7.4, "site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_template_tautomer", "his_B10": "neutral_template_tautomer" }, "fixed_group_charge_delta": -5, "net_formal_charge": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "hydrogen_delta_from_neutral_graph": -7, "interpretation": "Convenient conventional starting candidate under declared assumptions; it is neither a measured state nor ranked by a pKa or population calculation." }, "enumeration": { "state_count": 144, "factorization": { "macrocycle_carboxyl_groups": { "count": 3, "states_each": 2 }, "A_chain_N_terminus": { "count": 1, "states": [ "protonated", "neutral" ] }, "histidines": { "count": 2, "states_each": [ "neutral_template_tautomer", "neutral_alternate_tautomer", "protonated" ] } }, "net_formal_charge_counts": { "-8": 4, "-7": 20, "-6": 41, "-5": 44, "-4": 26, "-3": 8, "-2": 1 }, "net_formal_charge_range": [ -8, -2 ], "hydrogen_count_range": [ 453, 459 ], "probabilities_assigned": false, "states": [ { "state_index": 1, "state_id": "mcddd_a1p_h5t_h10t", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_template_tautomer", "his_B10": "neutral_template_tautomer" }, "histidine_tautomers": { "his_B5": "epsilon2", "his_B10": "epsilon2" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 2, "state_id": "mcddd_a1p_h5t_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_template_tautomer", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "epsilon2", "his_B10": "delta1" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 3, "state_id": "mcddd_a1p_h5t_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_template_tautomer", "his_B10": "protonated" }, "histidine_tautomers": { "his_B5": "epsilon2", "his_B10": "both_ring_nitrogens_protonated" }, "net_formal_charge": -6, "hydrogen_delta_from_neutral_graph": -6, "formula": "C325H455N79O97S6", "hydrogen_count": 455, "probability_assigned": false }, { "state_index": 4, "state_id": "mcddd_a1p_h5a_h10t", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_alternate_tautomer", "his_B10": "neutral_template_tautomer" }, "histidine_tautomers": { "his_B5": "delta1", "his_B10": "epsilon2" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 5, "state_id": "mcddd_a1p_h5a_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_alternate_tautomer", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "delta1", "his_B10": "delta1" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 6, "state_id": "mcddd_a1p_h5a_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "neutral_alternate_tautomer", "his_B10": "protonated" }, "histidine_tautomers": { "his_B5": "delta1", "his_B10": "both_ring_nitrogens_protonated" }, "net_formal_charge": -6, "hydrogen_delta_from_neutral_graph": -6, "formula": "C325H455N79O97S6", "hydrogen_count": 455, "probability_assigned": false }, { "state_index": 7, "state_id": "mcddd_a1p_h5p_h10t", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "protonated", "his_B10": "neutral_template_tautomer" }, "histidine_tautomers": { "his_B5": "both_ring_nitrogens_protonated", "his_B10": "epsilon2" }, "net_formal_charge": -6, "hydrogen_delta_from_neutral_graph": -6, "formula": "C325H455N79O97S6", "hydrogen_count": 455, "probability_assigned": false }, { "state_index": 8, "state_id": "mcddd_a1p_h5p_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "protonated", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "both_ring_nitrogens_protonated", "his_B10": "delta1" }, "net_formal_charge": -6, "hydrogen_delta_from_neutral_graph": -6, "formula": "C325H455N79O97S6", "hydrogen_count": 455, "probability_assigned": false }, { "state_index": 9, "state_id": "mcddd_a1p_h5p_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "protonated", "his_B5": "protonated", "his_B10": "protonated" }, "histidine_tautomers": { "his_B5": "both_ring_nitrogens_protonated", "his_B10": "both_ring_nitrogens_protonated" }, "net_formal_charge": -5, "hydrogen_delta_from_neutral_graph": -5, "formula": "C325H456N79O97S6", "hydrogen_count": 456, "probability_assigned": false }, { "state_index": 10, "state_id": "mcddd_a1n_h5t_h10t", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "neutral_template_tautomer", "his_B10": "neutral_template_tautomer" }, "histidine_tautomers": { "his_B5": "epsilon2", "his_B10": "epsilon2" }, "net_formal_charge": -8, "hydrogen_delta_from_neutral_graph": -8, "formula": "C325H453N79O97S6", "hydrogen_count": 453, "probability_assigned": false }, { "state_index": 11, "state_id": "mcddd_a1n_h5t_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "neutral_template_tautomer", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "epsilon2", "his_B10": "delta1" }, "net_formal_charge": -8, "hydrogen_delta_from_neutral_graph": -8, "formula": "C325H453N79O97S6", "hydrogen_count": 453, "probability_assigned": false }, { "state_index": 12, "state_id": "mcddd_a1n_h5t_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "neutral_template_tautomer", "his_B10": "protonated" }, "histidine_tautomers": { "his_B5": "epsilon2", "his_B10": "both_ring_nitrogens_protonated" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 13, "state_id": "mcddd_a1n_h5a_h10t", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "neutral_alternate_tautomer", "his_B10": "neutral_template_tautomer" }, "histidine_tautomers": { "his_B5": "delta1", "his_B10": "epsilon2" }, "net_formal_charge": -8, "hydrogen_delta_from_neutral_graph": -8, "formula": "C325H453N79O97S6", "hydrogen_count": 453, "probability_assigned": false }, { "state_index": 14, "state_id": "mcddd_a1n_h5a_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "neutral_alternate_tautomer", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "delta1", "his_B10": "delta1" }, "net_formal_charge": -8, "hydrogen_delta_from_neutral_graph": -8, "formula": "C325H453N79O97S6", "hydrogen_count": 453, "probability_assigned": false }, { "state_index": 15, "state_id": "mcddd_a1n_h5a_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "neutral_alternate_tautomer", "his_B10": "protonated" }, "histidine_tautomers": { "his_B5": "delta1", "his_B10": "both_ring_nitrogens_protonated" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 16, "state_id": "mcddd_a1n_h5p_h10t", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "protonated", "his_B10": "neutral_template_tautomer" }, "histidine_tautomers": { "his_B5": "both_ring_nitrogens_protonated", "his_B10": "epsilon2" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 17, "state_id": "mcddd_a1n_h5p_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "protonated", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "both_ring_nitrogens_protonated", "his_B10": "delta1" }, "net_formal_charge": -7, "hydrogen_delta_from_neutral_graph": -7, "formula": "C325H454N79O97S6", "hydrogen_count": 454, "probability_assigned": false }, { "state_index": 18, "state_id": "mcddd_a1n_h5p_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "deprotonated", "macrocycle_carboxyl_2": "deprotonated", "macrocycle_carboxyl_3": "deprotonated", "nterm_A1": "neutral", "his_B5": "protonated", "his_B10": "protonated" }, "histidine_tautomers": { 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}, "net_formal_charge": -4, "hydrogen_delta_from_neutral_graph": -4, "formula": "C325H457N79O97S6", "hydrogen_count": 457, "probability_assigned": false }, { "state_index": 143, "state_id": "mcppp_a1n_h5p_h10a", "variable_site_states": { "macrocycle_carboxyl_1": "protonated", "macrocycle_carboxyl_2": "protonated", "macrocycle_carboxyl_3": "protonated", "nterm_A1": "neutral", "his_B5": "protonated", "his_B10": "neutral_alternate_tautomer" }, "histidine_tautomers": { "his_B5": "both_ring_nitrogens_protonated", "his_B10": "delta1" }, "net_formal_charge": -4, "hydrogen_delta_from_neutral_graph": -4, "formula": "C325H457N79O97S6", "hydrogen_count": 457, "probability_assigned": false }, { "state_index": 144, "state_id": "mcppp_a1n_h5p_h10p", "variable_site_states": { "macrocycle_carboxyl_1": "protonated", "macrocycle_carboxyl_2": "protonated", "macrocycle_carboxyl_3": "protonated", "nterm_A1": "neutral", "his_B5": "protonated", "his_B10": "protonated" }, "histidine_tautomers": { "his_B5": 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"modified_PheB1_and_LysB29_nitrogens_remain_neutral": true, "canonical_candidate_is_charge_minus_7_and_formula_C325H454N79O97S6": true, "144_group_state_combinations_enumerated_without_probabilities": true, "charge_and_hydrogen_ranges_match_assumptions": true, "no_atom_localized_partial_charges_or_force_field_claimed": true }, "open_gates": [ "local pKa shifts and measured microstate populations", "atom-localized force-field charges and atom types for the NNC2215 conjugate", "histidine tautomer energetics and site-specific protonation", "tyrosine phenol sensitivity", "PheB1 hydrogen ownership and unique B29 coordinate map", "roof stereochemistry, solvent, counterions, and MD readiness" ] }